-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_9595605-9732003

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_24-snap.2038-T1
Valid prediction for GeneMark_model.94943_t
Couldn't classify 100349, 100481
Sorry, prediction pasa_asmbl_32536.p1 fails validation.
(ATG)	 AC	98291-98346	GT	CAG
(GAA)	 AG	99001-99044	GT	AGG
(GTC)	 AG	99135-99274	GT	TGG
(GCA)	 AG	99850-99945	GT	ATG
(GCA)	 AG	100127-100248	GT	AGG
(CAC)	 AG	100349-100481	GG	GTG
-recovered pasa_asmbl_32536.p1, initial, 98291, 98346
-recovered pasa_asmbl_32536.p1, internal, 99001, 99044
-recovered pasa_asmbl_32536.p1, internal, 99135, 99274
-recovered pasa_asmbl_32536.p1, internal, 99850, 99945
-recovered pasa_asmbl_32536.p1, internal, 100127, 100248
Valid prediction for snap_scaffold_24-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_54472-T1
Valid prediction for snap_scaffold_24-snap.2033-T1
Valid prediction for GeneMark_model.94946_t
Valid prediction for snap_scaffold_24-snap.2040-T1
Valid prediction for GlimmerHMM_glimmerT_54486-T1
Valid prediction for snap_scaffold_24-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_54480-T1
Valid prediction for GeneMark_model.94965_t
Valid prediction for GlimmerHMM_glimmerT_54474-T1
Valid prediction for pasa_asmbl_32529.p1
Valid prediction for HiQ_model.g36477.t1
Valid prediction for GeneMark_model.94949_t
Couldn't classify 84811, 84963
Sorry, prediction pasa_asmbl_32531.p2 fails validation.
(ATG)	 AG	83038-83202	GT	AGG
(GTG)	 AG	83365-83471	GT	CGG
(GTT)	 AG	83755-83876	GT	CGG
(ATC)	 AG	84041-84119	GT	AGG
(GAT)	 AG	84213-84383	GT	ATG
(GTA)	 AG	84555-84672	GT	AGG
(CTG)	 AG	84811-84963	TA	GGT
-recovered pasa_asmbl_32531.p2, initial, 83038, 83202
-recovered pasa_asmbl_32531.p2, internal, 83038, 83202
-recovered pasa_asmbl_32531.p2, internal, 83365, 83471
-recovered pasa_asmbl_32531.p2, internal, 83755, 83876
-recovered pasa_asmbl_32531.p2, internal, 84041, 84119
-recovered pasa_asmbl_32531.p2, internal, 84213, 84383
-recovered pasa_asmbl_32531.p2, internal, 84555, 84672
Valid prediction for Augustus_model.g36474.t1
Valid prediction for GlimmerHMM_glimmerT_54495-T1
Valid prediction for GeneMark_model.94955_t
Valid prediction for GlimmerHMM_glimmerT_54476-T1
Valid prediction for snap_scaffold_24-snap.2023-T1
Valid prediction for snap_scaffold_24-snap.2025-T1
Valid prediction for GlimmerHMM_glimmerT_54482-T1
Valid prediction for GlimmerHMM_glimmerT_54496-T1
Valid prediction for GeneMark_model.94952_t
Valid prediction for Augustus_model.g36479.t1
Valid prediction for Augustus_model.g36471.t1
Valid prediction for snap_scaffold_24-snap.2020-T1
Valid prediction for snap_scaffold_24-snap.2018-T1
Valid prediction for GeneMark_model.94947_t
Valid prediction for GlimmerHMM_glimmerT_54490-T1
Valid prediction for GeneMark_model.94957_t
Valid prediction for GlimmerHMM_glimmerT_54491-T1
Valid prediction for snap_scaffold_24-snap.2012-T1
Valid prediction for GeneMark_model.94919_t
Valid prediction for snap_scaffold_24-snap.2013-T1
Valid prediction for HiQ_model.g36480.t1
Valid prediction for GeneMark_model.94927_t
Valid prediction for CodingQuarry_transcript_37338-T1
Couldn't classify 83859, 83876
Couldn't classify 85092, 85098
Sorry, prediction pasa_asmbl_32533.p1 fails validation.
(TCT)	 CA	83859-83876	GT	CGG
(ATC)	 AG	84070-84119	GT	AGG
(GAT)	 AG	84213-84383	GT	ATG
(GTA)	 AG	84555-84672	GT	AGG
(CTG)	 AG	84811-84962	GT	AGG
(GTT)	 AG	85092-85098	GA	AGG
-recovered pasa_asmbl_32533.p1, internal, 84070, 84119
-recovered pasa_asmbl_32533.p1, internal, 84213, 84383
-recovered pasa_asmbl_32533.p1, internal, 84555, 84672
-recovered pasa_asmbl_32533.p1, internal, 84811, 84962
Valid prediction for GeneMark_model.94956_t
Valid prediction for GeneMark_model.94945_t
Valid prediction for GlimmerHMM_glimmerT_54477-T1
Valid prediction for GeneMark_model.94925_t
Valid prediction for GeneMark_model.94920_t
Valid prediction for GlimmerHMM_glimmerT_54484-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.94935_t
Valid prediction for GeneMark_model.94959_t
Valid prediction for snap_scaffold_24-snap.2026-T1
Valid prediction for GeneMark_model.94932_t
Valid prediction for snap_scaffold_24-snap.2016-T1
Valid prediction for GeneMark_model.94963_t
Valid prediction for GeneMark_model.94967_t
Valid prediction for snap_scaffold_24-snap.2035-T1
Valid prediction for GeneMark_model.94939_t
Valid prediction for GlimmerHMM_glimmerT_54487-T1
Valid prediction for GeneMark_model.94951_t
Valid prediction for GlimmerHMM_glimmerT_54492-T1
Valid prediction for Augustus_model.g36469.t1
Valid prediction for GeneMark_model.94953_t
Couldn't classify 87039, 87043
Sorry, prediction CodingQuarry_transcript_37340-T1 fails validation.
(ATG)	 CC	86248-86344	GC	CTG
(GCT)	 TC	87039-87043	AC	AGA
-recovered CodingQuarry_transcript_37340-T1, initial, 86248, 86344
Valid prediction for GeneMark_model.94929_t
Valid prediction for GlimmerHMM_glimmerT_54478-T1
Valid prediction for CodingQuarry_transcript_37339-T1
Valid prediction for GlimmerHMM_glimmerT_54485-T1
Valid prediction for snap_scaffold_24-snap.2039-T1
Couldn't classify 99853, 99945
Sorry, prediction pasa_asmbl_32537.p2 fails validation.
(GAC)	 CA	99853-99945	GT	ATG
(GCA)	 AG	100127-100248	GT	AGG
(CAC)	 AG	100349-100496	GT	AGG
(GGG)	 AG	100907-101028	GT	AGG
(GCA)	 AG	101498-101555	GA	GAG
-recovered pasa_asmbl_32537.p2, terminal, 101498, 101555
-recovered pasa_asmbl_32537.p2, internal, 100127, 100248
-recovered pasa_asmbl_32537.p2, internal, 100349, 100496
-recovered pasa_asmbl_32537.p2, internal, 100907, 101028
Valid prediction for GeneMark_model.94922_t
Valid prediction for GlimmerHMM_glimmerT_54475-T1
Valid prediction for GeneMark_model.94934_t
Valid prediction for GlimmerHMM_glimmerT_54488-T1
Valid prediction for snap_scaffold_24-snap.2028-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.94941_t
Valid prediction for GeneMark_model.94961_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GeneMark_model.94958_t
Valid prediction for snap_scaffold_24-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_54483-T1
Valid prediction for GeneMark_model.94926_t
Valid prediction for Augustus_model.g36478.t1
Valid prediction for GeneMark_model.94942_t
Valid prediction for snap_scaffold_24-snap.2034-T1
Valid prediction for snap_scaffold_24-snap.2024-T1
Valid prediction for GlimmerHMM_glimmerT_54481-T1
Valid prediction for Augustus_model.g36470.t1
Couldn't classify 21444, 21527
Sorry, prediction pasa_asmbl_33138.p1 fails validation.
(ATG)	 AG	19938-20003	GT	AGG
(CTG)	 AG	20216-20319	GT	TGG
(GCC)	 AG	20510-20675	GT	AGG
(ATG)	 AG	21444-21527	AG	TTA
-recovered pasa_asmbl_33138.p1, initial, 19938, 20003
-recovered pasa_asmbl_33138.p1, internal, 19938, 20003
-recovered pasa_asmbl_33138.p1, internal, 20216, 20319
-recovered pasa_asmbl_33138.p1, internal, 20510, 20675
Valid prediction for Augustus_model.g36475.t1
Valid prediction for snap_scaffold_24-snap.2037-T1
Valid prediction for GeneMark_model.94954_t
Valid prediction for GeneMark_model.94968_t
Valid prediction for GlimmerHMM_glimmerT_54498-T1
Valid prediction for GlimmerHMM_glimmerT_54499-T1
Valid prediction for GeneMark_model.94931_t
Valid prediction for GeneMark_model.94921_t
Valid prediction for GeneMark_model.94960_t
Valid prediction for snap_scaffold_24-snap.2029-T1
Valid prediction for GeneMark_model.94924_t
Valid prediction for GeneMark_model.94928_t
Valid prediction for GeneMark_model.94944_t
Couldn't classify 45738, 45836
Sorry, prediction pasa_asmbl_33134.p1 fails validation.
(ATG)	 AC	43519-43743	GT	AGG
(GCT)	 AG	43944-44060	GT	AGG
(GCA)	 AG	44228-44303	GT	AGG
(ACC)	 AG	44779-44948	GT	AGG
(GTG)	 AG	45251-45361	GT	AGG
(GAG)	 AG	45738-45836	GT	GCG
-recovered pasa_asmbl_33134.p1, initial, 43519, 43743
add_exon() Sorry, pasa_asmbl_33134.p1 44228-44303-terminal-3 is invalid.
-recovered pasa_asmbl_33134.p1, terminal, 44228, 44303
-recovered pasa_asmbl_33134.p1, internal, 43944, 44060
-recovered pasa_asmbl_33134.p1, internal, 44228, 44303
-recovered pasa_asmbl_33134.p1, internal, 44779, 44948
-recovered pasa_asmbl_33134.p1, internal, 45251, 45361
-recovered pasa_asmbl_33134.p1, internal, 45738, 45836
Valid prediction for snap_scaffold_24-snap.2019-T1
Valid prediction for GeneMark_model.94938_t
Valid prediction for snap_scaffold_24-snap.2030-T1
Couldn't classify 5078, 5188
Couldn't classify 7201, 7233
Sorry, prediction pasa_asmbl_33272.p1 fails validation.
(GGC)	 AG	5078-5188	GT	AGG
(TAC)	 AG	5474-5563	GT	AGG
(CTG)	 AG	6718-6798	GT	AGG
(GGC)	 AG	6905-7012	GT	GGG
(GTT)	 AG	7201-7233	AC	AGA
-recovered pasa_asmbl_33272.p1, internal, 5078, 5188
-recovered pasa_asmbl_33272.p1, internal, 5474, 5563
-recovered pasa_asmbl_33272.p1, internal, 6718, 6798
-recovered pasa_asmbl_33272.p1, internal, 6905, 7012
Valid prediction for GlimmerHMM_glimmerT_54494-T1
Couldn't classify 67938, 68152
Couldn't classify 68594, 68678
Sorry, prediction pasa_asmbl_33293.p2 fails validation.
(TCT)	 CA	67938-68152	GT	ATG
(AGA)	 AG	68594-68678	TC	TGT
Valid prediction for GlimmerHMM_glimmerT_54473-T1
Valid prediction for Augustus_model.g36481.t1
Valid prediction for snap_scaffold_24-snap.2027-T1
Valid prediction for snap_scaffold_24-snap.2041-T1
Valid prediction for GlimmerHMM_glimmerT_54493-T1
Couldn't classify 9099, 9136
Couldn't classify 16309, 16430
Sorry, prediction pasa_asmbl_33139.p1 fails validation.
(CGG)	 GA	9099-9136	GT	AGG
(GCC)	 AG	9280-9344	GT	CGG
(GCG)	 AG	9443-9524	GT	AAG
(GTC)	 AG	9861-10011	GT	AGG
(ATC)	 AG	10872-11069	GT	AGG
(GTG)	 AG	11170-11328	GT	TGG
(AGC)	 AG	11513-11694	GT	AGG
(GAT)	 AG	11889-11957	GT	AAG
(ATA)	 AG	12042-12115	GT	AGG
(GGG)	 AG	12258-12361	GT	TGG
(AAG)	 AG	12980-13161	GT	AAG
(GCT)	 AG	14168-14371	GT	AGG
(GAT)	 AG	15671-15824	GT	AGG
(GTG)	 AG	16071-16173	GT	AGG
(GGA)	 AG	16309-16430	CT	CCC
add_exon() Sorry, pasa_asmbl_33139.p1 16071-16173-terminal-3 is invalid.
-recovered pasa_asmbl_33139.p1, terminal, 16071, 16173
-recovered pasa_asmbl_33139.p1, internal, 9280, 9344
-recovered pasa_asmbl_33139.p1, internal, 9443, 9524
-recovered pasa_asmbl_33139.p1, internal, 9861, 10011
-recovered pasa_asmbl_33139.p1, internal, 10872, 11069
-recovered pasa_asmbl_33139.p1, internal, 11170, 11328
-recovered pasa_asmbl_33139.p1, internal, 11513, 11694
-recovered pasa_asmbl_33139.p1, internal, 11889, 11957
-recovered pasa_asmbl_33139.p1, internal, 12042, 12115
-recovered pasa_asmbl_33139.p1, internal, 12258, 12361
-recovered pasa_asmbl_33139.p1, internal, 12980, 13161
-recovered pasa_asmbl_33139.p1, internal, 14168, 14371
-recovered pasa_asmbl_33139.p1, internal, 15671, 15824
-recovered pasa_asmbl_33139.p1, internal, 16071, 16173
Valid prediction for Augustus_model.g36472.t1
Valid prediction for GeneMark_model.94969_t
Valid prediction for GlimmerHMM_glimmerT_54489-T1
Valid prediction for GlimmerHMM_glimmerT_54479-T1
Valid prediction for GeneMark_model.94937_t
Valid prediction for snap_scaffold_24-snap.2017-T1
Valid prediction for GeneMark_model.94948_t
Valid prediction for Augustus_model.g36476.t1
Valid prediction for GeneMark_model.94940_t
Valid prediction for GeneMark_model.94930_t
Valid prediction for snap_scaffold_24-snap.2036-T1
Valid prediction for GeneMark_model.94966_t
Valid prediction for GeneMark_model.94962_t
Valid prediction for GeneMark_model.94950_t
Valid prediction for snap_scaffold_24-snap.2031-T1
Valid prediction for GeneMark_model.94936_t
Valid prediction for GeneMark_model.94964_t
Valid prediction for snap_scaffold_24-snap.2032-T1
Valid prediction for Augustus_model.g36473.t1
Valid prediction for GeneMark_model.94923_t
Valid prediction for GlimmerHMM_glimmerT_54497-T1
Valid prediction for snap_scaffold_24-snap.2015-T1
Valid prediction for GeneMark_model.94933_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25505, rend_intergenic: 15653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32291, rend_intergenic: 28846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37994, rend_intergenic: 33839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40972, rend_intergenic: 38108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58832, rend_intergenic: 55895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69514, rend_intergenic: 65503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88502, rend_intergenic: 81787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93955, rend_intergenic: 92292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97699, rend_intergenic: 94886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105225, rend_intergenic: 99136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132142, rend_intergenic: 109877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136399
-exon list size: 663


building trellis

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59.8    
60.0    
60.2    
60.3    
60.5    
60.6    
60.8    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 25505, rend_intergenic: 15653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32291, rend_intergenic: 28846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37994, rend_intergenic: 33839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40972, rend_intergenic: 38108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58832, rend_intergenic: 55895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69514, rend_intergenic: 65503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88502, rend_intergenic: 81787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93955, rend_intergenic: 92292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97699, rend_intergenic: 94886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105225, rend_intergenic: 99136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132142, rend_intergenic: 109877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support